Michael Lerner, Ph.D.

Associate professor of physics and engineering

Email:[email protected]

Department: Physics and Astronomy

Program: Pre-Engineering

Location: Center for Science and Technology Room 213
801 National Road
Richmond, Indiana 47374

About me

I am a computational biophysicist who studies membranes, lipids, nucleic acids, proteins and dynamics to examine problems from basic physics to drug design. I often collaborate with students on research projects.

I help out with the men’s and women’s Ultimate Frisbee teams every spare moment that I get! I also enjoy cooking, spending time with my wife and three young children. I also enjoy power lifting, although perhaps that’s not fair, as it provides some good examples for my physics classes.

Somewhere in the middle of my undergraduate career, I decided that I wanted to become a professor at a small, liberal arts college. I’ve tried several different careers (from volunteering in inner-city public schools in Chicago with City Year, to working as a computer programmer in the Bay Area during the dot-com boom), but my passion for both teaching and research kept bringing me back to academia. Earlham is the rare place that cares about all community members as people with both academic and non-academic lives, that brings the liberal arts to life in a modern setting, that values teaching excellence alongside research, and that holds Quaker ideals dear. In my experience, our students are all here because they are passionate about something. Even my introductory classes are entirely full of students who genuinely want to learn and explore, and I rarely run into a student who is just taking a class to check off a requirement. Earlham is a small, relatively intimate community, and I’ve found that literally every single student I’ve gotten to know has been an interesting, good person.


  • Ph.D., University of Michigan, Ann Arbor
  • M.S., University of Michigan, Ann Arbor
  • B.S., Haverford College

Professional memberships

Scholarly interest

I am a computational biophysicist (translation: I like to think like a physicist, think about problems motivated by biology and use simulations as a “computational microscope” with which to examine the world). I study membranes, lipids, nucleic acids, proteins and dynamics to examine problems from basic physics to drug design.

Research projects

  • Molecular Dynamics
  • Diffusion of proteins and lipids within membranes
  • Protein structure and dynamics
  • Nucleic acid structure
  • Computational Topology Drug design

Collaborative student research experiences

While most of the DNA structures that you see in textbooks are right-handed helices called B-DNA, it turns out that DNA can also be found in a left-handed helix, called Z-DNA. This left-handed form is important for relieving torsional strain, and is likely also involved in diverse parts of biochemistry ranging from gene regulation to Alzheimer’s disease. Surprisingly, the biochemical process by which B-DNA is transformed into Z-DNA is still not well understood. Due to the size of the systems involved, direct experimental measurements range from hard to impossible. Our group works with physics, chemistry, computer science and biochemistry students to use computational models to understand this transition.

Published works

“Single molecule diffusion of membrane-bound proteins: Window into lipid contacts and bilayer dynamics”   Jefferson D. Knight, Michael G. Lerner, Joan G. Marcano-Velazquez, Richard W. Pastor and Joseph J. Falke   Biophysical Journal 99(9):2870-2887 (2010)

“Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design”  Michael G. Lerner, Kristin L. Meagher and Heather A. Carlson  Journal of Computer-aided Molecular Design 22(10):727-736 (2008)

“Protein Flexibility and Species Specificity in Structure-Based Drug Discovery: Dihydrofolate Reductase as a Test System” Anna L. Bowman, Michael G. Lerner and Heather A. Carlson  Journal of the American Chemical Society 129(12):48109-1065 (2007)

“Incorporating Dynamics in E. coli Dihydrofolate Reductase Enhances Structure-Based Drug Discovery” Michael G. Lerner, Anna L. Bowman and Heather A. Carlson  Journal of Chemical Information and Modeling 47(6):2358-2365 (2007)

“Refining the Multiple Protein Structure Pharmacophore Method: Consistency across Three Independent HIV-1 Protease Models” Kristin L. Meagher, Michael G. Lerner and Heather A. Carlson  Journal of Medicinal Chemistry 49(12):3478-3484 (2006)

“Binding MOAD (mother of all databases)”  Leigi Hu, Mark L. Benson, Richard D. Smith, Michael G. Lerner and Heather A. Carlson Proteins: Structure, Function and Bioinformatics 60:333-340 (2005)

Recent poster presentations ([*] denotes research with Earlham Undergraduates):

“Molecular Dynamics Studies of Z[WC] DNA and the B to Z-DNA Transition” Michael G. Lerner, Jinhee Kim[*], Alexander K. Seewald[*]  Biophysical Society Meeting, San Francisco, 2014   

“Non-equilibrium Computation of Diffusion Constants for Water, Lipids and Proteins” Michael G. Lerner, Hoang Tran[*]  Biophysical Society Meeting, San Francisco, 2014   

“Teaching the Jarzynski equality with parallel computing” Michael G. Lerner, Laboratory Instruction Beyond the First Year of College, Philadelphia, 2012